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1 Intro

This report provides some basic description of the peptide identificaiton from database search. Users can use this to quickly check the overal quality of the experiment Users can download the clean peptide quantification matrix for downstream analysis

2 Take-home figures

  • Number of contaminant: 27

  • Number of reversed: 52

  • Number of qualified peptides: 16313

  • Number of quailfied peptide without intensity information(0 intensitiy): 695

  • Number of experiment: 24

  • All experiments: Xu_MLIspin_test_B6, Xu_MLIspin_test_B7, Xu_MLIspin_test_B8, Xu_MLIspin_test_B9, Xu_MLIspin_test_C6, Xu_MLIspin_test_C7, Xu_MLIspin_test_C8, Xu_MLIspin_test_C9, Xu_MLIspin_test_D6, Xu_MLIspin_test_D7, Xu_MLIspin_test_D8, Xu_MLIspin_test_D9, Xu_MLIspin_test_E6, Xu_MLIspin_test_E7, Xu_MLIspin_test_E8, Xu_MLIspin_test_E9, Xu_MLIspin_test_F6, Xu_MLIspin_test_F7, Xu_MLIspin_test_F8, Xu_MLIspin_test_F9, Xu_MLIspin_test_G6, Xu_MLIspin_test_G7, Xu_MLIspin_test_G8, Xu_MLIspin_test_G9

  • No meta information provided

3 Peptide Charge States

Why charge state?

  1. Peptide Charge distribution is a good sign of trypsin digestion and electric spray ionization.

  • In a typical ESI analysis of trytic digest, most of the peptides should have 2 charges, less peptides have 3 charges, because tryptic peptides have a lysine/arginie at the C-terminal, along with N-terminal contributing another charge. A possible miscleavage will contribute the third charge.

    • In a ESI procedure, peptides with 2 and more charges are easier to fragment and then identified by MS. However, too mnay charges will make the m/z of the peptide too small to escape the scan range, further more, it will also complicate the ms2 spectra.
  1. if you see more peptides with charge 3 than charge 2 state,

  • It might indcate in-sufficient trypsin digesion, check the percentage of peptides with mis-cleavage site.

  • It migtht indcate the ESI is not sufficient/good enough.Check the distance between the ESI tip and MS oriface, if the ESI tip is dirty, if there is droplet occasionally.

4 Peptide Length

Why peptide length do you expect?

  • Averge length of tryptic peptide is around 10.
    • refer to this page for peptide length.
    • https://www.hindawi.com/journals/isrn/2014/960902/fig3/

5 Peptide Score distribution

Why peptide length do you expect?

  • The average score should be around 50

6 Quantification Sparsity Distrubition

In most cases, label-free quantification provides a decent way for metaproteomics profiling.

6.1 Sparsity Profile

The more peptide of 100% presence the better

6.2 Sparsity cummulative curve

Figure shows how many peptides have more than N presence, which helps to set the presence cutoff

7 Peptide Intensity disitribution across samples/experiments

8 Overall Expression Profile

8.1 Heatmap

8.1.1 Heatmap of Q100 peptides (with 100% presence across experiments)

8.1.2 Heatmap of Top 100 Intensity peptides

9 PCA Analysis

10 Download the neat table

The table is clean peptides expression table, with reversed and contaminant removed. The values are the LFQ(with label free quantification turned on) or raw protein intensity from Maxquant output. You can download/export and start from this table for downstream analysis using the (i)Metalab faminly apps.

The talbe can be further visualized by our shiny apps shiny.imetalab.ca